Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation

Abstract

Different combinations and permutations of transcription factors work together to regulate the expression of target genes. These proteins often contain high levels of intrinsically disordered regions, which are important mediators of protein{ extendash}protein interactions. We show that unusual binding kinetics associated with an intrinsically disordered region in a transcriptional coregulator can regulate the formation of transcriptional complexes that lead to the specification of neuronal cell subtypes. Notably, a single intrinsically disordered region shows selective differences in binding kinetics for proteins of the same family, which have implications for how intrinsic disorder contributes to regulatory processes and complexity in higher organisms.Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein{ extendash}protein interactions within these complexes are mediated by ordered LIM domains in the LIM-HD proteins and intrinsically disordered LIM interaction domains (LIDs) in LDB1 and ISL1; however, little is known about how the strength or rates of binding contribute to complex assemblies. We have measured the interactions of LIM:LID complexes using FRET-based protein{ extendash}protein interaction studies and EMSAs and used these data to model population distributions of complexes. The protein{ extendash}protein interactions within the ternary complexes are much weaker than those in the binary complex, yet surprisingly slow LDB1:ISL1 dissociation kinetics and a substantial increase in DNA binding affinity promote formation of the ternary complex over the binary complex in motor neurons. We have used mutational and protein engineering approaches to show that allostery and modular binding by tandem LIM domains contribute to the LDB1LID binding kinetics. The data indicate that a single intrinsically disordered region can achieve highly disparate binding kinetics, which may provide a mechanism to regulate the timing of transcriptional complex assembly.

Publication
Proceedings of the National Academy of Sciences, (115), 18, pp. 4643–4648, https://doi.org/10.1073/pnas.1714646115
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